Modelling and Stochastic Simulation of Synthetic Biological Boolean Gates

Sanassy, Daven; Fellermann, Harold; Krasnogor, Natalio; Konur, Savas; Mierlă, Laurenţiu; Gheorghe, Marian; Ladroue, Christophe; Kalvala, Sara

doi:10.1109/hpcc.2014.68

Cited by 18 publications

(13 citation statements)

References 16 publications

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“…The platform intends to facilitate the design, simulation, verification, and ultimately the rapid prototyping of synthetic biological systems [67].…”

Section: Discussionmentioning

confidence: 99%

Formalizing Modularization and Data Hiding in Synthetic Biology

Fellermann

Hadorn²,

Füchslin

et al. 2014

J. Emerg. Technol. Comput. Syst.

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Biological systems employ compartmentalization and other co-localization strategies in order to orchestrate a multitude of biochemical processes by simultaneously enabling "data hiding" and modularization. This paper presents recent research that embraces compartmentalization and co-location as an organizational programmatic principle in synthetic biological and biomimetic systems. In these systems, artificial vesicles and synthetic minimal cells are envisioned as nanoscale reactors for programmable biochemical synthesis and as chassis for molecular information processing. We present P systems, brane calculi, and the recently developed chemtainer calculus as formal frameworks providing data hiding and modularization and thus enabling the representation of highly complicated hierarchically organized compartmentalized reaction systems. We demonstrate how compartmentalization can greatly reduce the complexity required to implement computational functionality, and how addressable compartments permit the scaling-up of programmable chemical synthesis.

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“…The platform intends to facilitate the design, simulation, verification, and ultimately the rapid prototyping of synthetic biological systems [67].…”

Section: Discussionmentioning

confidence: 99%

Formalizing Modularization and Data Hiding in Synthetic Biology

Fellermann

Hadorn²,

Füchslin

et al. 2014

J. Emerg. Technol. Comput. Syst.

Self Cite

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“…The properties expressed in kP-Queries are verified using the Spin [13] The simulation component features a native simulator [2,19], which allows the users to simulate kP system models efficiently. In addition, kPWorkbench integrates the Flame simulator [4,23], a general purpose large scale agent based simulation environment, based on a method that allows users to express kP systems as a set of communicating X-machines [11].…”

Section: Kpworkbenchmentioning

confidence: 99%

“…quorum sensing [18], genetic Boolean gates [23] and synthetic pulse generators [1], to some classical computational problems, e.g. sorting [6], broadcasting [10] and subset sum [5].…”

Section: Introductionmentioning

confidence: 99%

Modelling and Validating an Engineering Application in Kernel P Systems

et al. 2017

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Abstract. This paper illustrates how kernel P systems (kP systems) can be used for modelling and validating an engineering application, in this case a cruise control system of an electric bike. The validity of the system is demonstrated via formal verification, carried out using the kPWorkbench tool. Furthermore, we show how the kernel P system model can be tested using automata and X-machine based techniques.

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“…One such membrane computing model is kernel P systems (kP systems, for short), introduced in [4,5]. kP systems are widely used in various applications, ranging from systems and synthetic biology to engineering applications [6][7][8][9][10][11][12]. It allows models to be simulated and formally verified using third party model checkers using a software framework, called kPWorkbench [13].…”

Section: Introductionmentioning

confidence: 99%

Search-based testing in membrane computing

et al. 2019

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Search-based testing is widely used for generating test sets. It is also applied in the case of model-based testing, especially for (extended) finite state machines. In this paper, we define such an approach for kernel P system models. We consider a specific kernel P system model and a define a search-based testing method. The test set generated consists of input sequences producing a given computation defined by the model. An example illustrates the use of the introduced method.

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Modelling and Stochastic Simulation of Synthetic Biological Boolean Gates

Cited by 18 publications

References 16 publications

Formalizing Modularization and Data Hiding in Synthetic Biology

Formalizing Modularization and Data Hiding in Synthetic Biology

Modelling and Validating an Engineering Application in Kernel P Systems

Search-based testing in membrane computing

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